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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ), 'gf_id' => 'HOM05D001270', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001270' ), 'data_identifier' => 'HOM05D001270', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001270', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12910' => 'bna', 'A08p34010' => 'bna', 'A08p34140' => 'bna', 'A10p08690' => 'bna', 'Aa31LG1G4530' => 'aar', 'Aa31LG9G16030' => 'aar', 'Aa31sc221G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3902' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3280' => 'aag', 'Actinidia01173' => 'ach', 'Actinidia12731' => 'ach', 'Actinidia14053' => 'ach', 'Actinidia14054' => 'ach', 'Actinidia21866' => 'ach', 'Actinidia22387' => 'ach', 'Actinidia33822' => 'ach', 'Actinidia37537' => 'ach', 'Actinidia38791' => 'ach', 'Ah.01g014570' => 'amhyb', 'Ah.02g131810' => 'amhyb', 'Ah.08g217560' => 'amhyb', 'Ah.15g094730' => 'amhyb', 'Ah.15g094740' => 'amhyb', 'AL1G20870' => 'aly', 'AL1G21140' => 'aly', 'AL8G23800' => 'aly', 'Aqoxy1G01475' => 'aox', 'Aqoxy1G03077' => 'aox', 'Aqoxy3G03202' => 'aox', 'Aqoxy5G00173' => 'aox', 'Aqoxy7G02471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.M2J0L9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RB1MXI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZ5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCXV2P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1USIG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4J9LG' => 'arhy', 'AT1G10180' => 'ath', 'AT1G10385' => 'ath', 'AT5G49830' => 'ath', 'ATR0736G211' => 'atr', 'ATR0743G240' => 'atr', 'ATR0763G097' => 'atr', 'Atru.chr1.2778' => 'acertr', 'Atru.chr11.1886' => 'acertr', 'Atru.chr13.2017' => 'acertr', 'Atru.chr5.1788' => 'acertr', 'Atru.chr5.1797' => 'acertr', 'AUR62001374' => 'cqu', 'AUR62025054' => 'cqu', 'AUR62025590' => 'cqu', 'AUR62026297' => 'cqu', 'AUR62026491' => 'cqu', 'AUR62037137' => 'cqu', 'BcaB08g35338' => 'bca', 'BcaC04g20833' => 'bca', 'BcaC07g38552' => 'bca', 'BcaC07g38554' => 'bca', 'BolC8t48975H' => 'bol', 'BolC8t49003H' => 'bol', 'BolC9t56723H' => 'bol', 'BraA02t06345Z' => 'bra', 'BraA08t35314Z' => 'bra', 'BraA08t35326Z' => 'bra', 'BraSC37t46132Z' => 'bra', 'C08p13450' => 'bna', 'C08p13650' => 'bna', 'C09p38690' => 'bna', 'CAN.G1222.18' => 'can', 'CAN.G1270.2' => 'can', 'CAN.G659.10' => 'can', 'CAN.G659.11' => 'can', 'CAN.G790.26' => 'can', 'CANSAT01G0064' => 'cansat', 'CANSAT01G0330' => 'cansat', 'CANSAT01G2720' => 'cansat', 'CANSAT01G2829' => 'cansat', 'CANSAT35G0483' => 'cansat', 'CANSAT35G1995' => 'cansat', 'CARHR010280' => 'chi', 'CARHR010520' => 'chi', 'CARHR258890' => 'chi', 'Carub.0001s0959' => 'cru', 'Carub.0001s0981' => 'cru', 'Carub.0008s0971' => 'cru', 'Ca_09657_v3' => 'car', 'Ca_18770_v3' => 'car', 'Ca_20946_v3' => 'car', 'Ca_25742_v3' => 'car', 'CBR_g38266' => 'cbr', 'Cc01_g18000' => 'ccan', 'Cc04_g00400' => 'ccan', 'Cc09_g06340' => 'ccan', 'Cc11_g13780' => 'ccan', 'CDE05G2053' => 'cde', 'CDE05G2683' => 'cde', 'CDE05G3672' => 'cde', 'CDE12G0568' => 'cde', 'Cfa000724' => 'cfa', 'Cfa002128' => 'cfa', 'Cfa002465' => 'cfa', 'Cfa009052' => 'cfa', 'Ciclev10014354m.g' => 'ccl', 'Ciclev10018912m.g' => 'ccl', 'Ciclev10024953m.g' => 'ccl', 'Ciclev10033337m.g' => 'ccl', 'CiPaw.01G088400' => 'cil', 'CiPaw.02G051100' => 'cil', 'CiPaw.06G078900' => 'cil', 'CiPaw.09G078800' => 'cil', 'CiPaw.10G065200' => 'cil', 'ClCG01G009310' => 'cla', 'ClCG07G001260' => 'cla', 'ClCG08G009040' => 'cla', 'ClCG09G001470' => 'cla', 'COL.COLO4_09583' => 'col', 'COL.COLO4_22869' => 'col', 'COL.COLO4_22870' => 'col', 'COL.COLO4_22871' => 'col', 'COL.COLO4_30979' => 'col', 'COL.COLO4_36235' => 'col', 'COL.COLO4_36582' => 'col', 'Cpa.g.sc135.33' => 'cpa', 'Cpa.g.sc165.42' => 'cpa', 'Cpa.g.sc173.10' => 'cpa', 'Cpa.g.sc173.11' => 'cpa', 'Cpa.g.sc5.299' => 'cpa', 'Cre12.g539050' => 'cre', 'CsaV3_1G046570' => 'csa', 'CsaV3_3G028190' => 'csa', 'CsaV3_6G036110' => 'csa', 'CsaV3_7G033850' => 'csa', 'CSS0029326' => 'camsi', 'CSS0035643' => 'camsi', 'CSS0038539' => 'camsi', 'CSS0041576' => 'camsi', 'CSS0042607' => 'camsi', 'CSS0044778' => 'camsi', 'DCAR_000589' => 'dca', 'DCAR_001326' => 'dca', 'DCAR_022627' => 'dca', 'DCAR_024500' => 'dca', 'Dinv20360' => 'din', 'Dinv30568' => 'din', 'Dinv31152' => 'din', 'Dinv34657' => 'din', 'Dinv37800' => 'din', 'Duzib192G0149' => 'dzi', 'Duzib192G0897' => 'dzi', 'Duzib211G0090' => 'dzi', 'Duzib235G0277' => 'dzi', 'Duzib235G0528' => 'dzi', 'Duzib268G0923' => 'dzi', 'ECA232G1315' => 'eca', 'ECA234G2103' => 'eca', 'ECA234G2436' => 'eca', 'ECA236G3866' => 'eca', 'EL10Ac4g08648' => 'bvu', 'EL10Ac6g13119' => 'bvu', 'EL10Ac7g18231' => 'bvu', 'Eucgr.A01365' => 'egr', 'Eucgr.B03396' => 'egr', 'Eucgr.E01884' => 'egr', 'Eucgr.E01893' => 'egr', 'Eucgr.F04008' => 'egr', 'FAN02G2484' => 'fan', 'FAN05G5284' => 'fan', 'FAN07G1564' => 'fan', 'FAN09G0450' => 'fan', 'FAN11G3473' => 'fan', 'FAN12G1197' => 'fan', 'FAN14G1090' => 'fan', 'FAN15G0294' => 'fan', 'FAN15G1943' => 'fan', 'FAN16G1245' => 'fan', 'FAN17G0879' => 'fan', 'FAN20G2190' => 'fan', 'FAN21G2144' => 'fan', 'FAN22G1295' => 'fan', 'FAN23G1154' => 'fan', 'FAN25G3120' => 'fan', 'FAN27G2467' => 'fan', 'FvH4_2g20870' => 'fve', 'FvH4_3g12130' => 'fve', 'FvH4_4g35500' => 'fve', 'FvH4_6g37400' => 'fve', 'Glyma.01G039700' => 'gma', 'Glyma.02G025100' => 'gma', 'Glyma.07G003600' => 'gma', 'Glyma.07G222800' => 'gma', 'Glyma.08G223000' => 'gma', 'Glyma.10G039400' => 'gma', 'Glyma.20G021700' => 'gma', 'Gohir.A03G145100' => 'ghi', 'Gohir.A05G113600' => 'ghi', 'Gohir.A06G142333' => 'ghi', 'Gohir.A10G007500' => 'ghi', 'Gohir.A11G132500' => 'ghi', 'Gohir.D02G168450' => 'ghi', 'Gohir.D02G168500' => 'ghi', 'Gohir.D05G114000' => 'ghi', 'Gohir.D06G145200' => 'ghi', 'Gohir.D10G007400' => 'ghi', 'Gohir.D11G138600' => 'ghi', 'Gorai.005G188900' => 'gra', 'Gorai.007G148700' => 'gra', 'Gorai.009G118000' => 'gra', 'Gorai.010G168900' => 'gra', 'Gorai.011G008100' => 'gra', 'GSVIVG01012095001' => 'vvi', 'GSVIVG01016127001' => 'vvi', 'GSVIVG01016128001' => 'vvi', 'GSVIVG01020112001' => 'vvi', 'HanXRQChr04g0111321' => 'han', 'HanXRQChr10g0311541' => 'han', 'HanXRQChr12g0359931' => 'han', 'HanXRQChr13g0399981' => 'han', 'HanXRQChr14g0446501' => 'han', 'HanXRQChr15g0487341' => 'han', 'Haze_06022' => 'cav', 'Haze_06023' => 'cav', 'Haze_06025' => 'cav', 'Haze_12085' => 'cav', 'Haze_16312' => 'cav', 'Haze_24677' => 'cav', 'Haze_24685' => 'cav', 'Hma1.2p1_0040F.1_g025050' => 'hma', 'Hma1.2p1_0090F.1_g045550' => 'hma', 'Hma1.2p1_0289F.1_g114390' => 'hma', 'Hma1.2p1_0289F.1_g114410' => 'hma', 'Hma1.2p1_1104F.1_g257390' => 'hma', 'HPP92_010125' => 'vpl', 'HPP92_012437' => 'vpl', 'HPP92_012533' => 'vpl', 'HPP92_012835' => 'vpl', 'Hund05688' => 'sun', 'Hund18622' => 'sun', 'Hund25288' => 'sun', 'Lalb_Chr01g0011761' => 'lal', 'Lalb_Chr05g0219751' => 'lal', 'Lalb_Chr16g0382681' => 'lal', 'Lalb_Chr16g0382691' => 'lal', 'Lalb_Chr16g0385291' => 'lal', 'Lj1A71T64' => 'lonja', 'Lj1C1143G4' => 'lonja', 'Lj1g0013875' => 'lja', 'Lj2g0022375' => 'lja', 'Lj3C1044T3' => 'lonja', 'Lj3g0015311' => 'lja', 'Lj4g0019362' => 'lja', 'Lj5A25G39' => 'lonja', 'Lj5g0003890' => 'lja', 'Lj6A20T7' => 'lonja', 'Lj6A3T44' => 'lonja', 'Lj6A3T45' => 'lonja', 'Lj6A4T7' => 'lonja', 'Lj6A7T9' => 'lonja', 'Lsat_1_v5_gn_1_46441' => 'lsa', 'Lsat_1_v5_gn_5_137500' => 'lsa', 'Lsat_1_v5_gn_7_2420' => 'lsa', 'Lsat_1_v5_gn_7_25041' => 'lsa', 'Lsat_1_v5_gn_8_117740' => 'lsa', 'Lsat_1_v5_gn_8_141481' => 'lsa', 'Lsat_1_v5_gn_8_160721' => 'lsa', 'Manes.01G193100' => 'mes', 'Manes.04G064700' => 'mes', 'Manes.12G035300' => 'mes', 'Manes.16G059300' => 'mes', 'Mapoly0120s0028' => 'mpo', 'MBI04_g19167_MAGBIO' => 'mbi', 'MBI07_g22364_MAGBIO' => 'mbi', 'MBI18_g24223_MAGBIO' => 'mbi', 'MCO14G008' => 'mco', 'MD05G1192300' => 'mdo', 'MD05G1254700' => 'mdo', 'MD09G1158400' => 'mdo', 'MD10G1234800' => 'mdo', 'MD13G1082700' => 'mdo', 'MD17G1144400' => 'mdo', 'Medtr1g069620' => 'mtr', 'Medtr1g111120' => 'mtr', 'Medtr2g022500' => 'mtr', 'Medtr4g005930' => 'mtr', 'Medtr4g083940' => 'mtr', 'Medtr6g045363' => 'mtr', 'MELO3C012853.2' => 'cme', 'MELO3C021771.2' => 'cme', 'MELO3C024298.2' => 'cme', 'MELO3C026501.2' => 'cme', 'Migut.D00460' => 'egut', 'Migut.I01174' => 'egut', 'Migut.L01366' => 'egut', 'Migut.M01970' => 'egut', 'MSTRG.10895' => 'ama', 'MSTRG.16338' => 'ama', 'Nitab4.5_0002056g0040' => 'nta', 'Nitab4.5_0002389g0070' => 'nta', 'Nitab4.5_0002885g0100' => 'nta', 'Nitab4.5_0003295g0130' => 'nta', 'Nitab4.5_0003773g0090' => 'nta', 'Nitab4.5_0004372g0030' => 'nta', 'Nitab4.5_0004372g0040' => 'nta', 'Nitab4.5_0004372g0050' => 'nta', 'Nitab4.5_0004372g0060' => 'nta', 'Nitab4.5_0004372g0070' => 'nta', 'Nitab4.5_0004857g0020' => 'nta', 'Nn2g12607' => 'nnu', 'Nn3g17077' => 'nnu', 'Nn3g17264' => 'nnu', 'Nn7g38124' => 'nnu', 'Nn8g40307' => 'nnu', 'Oeu029616.1' => 'oeu', 'Oeu040351.1' => 'oeu', 'Oeu040352.1' => 'oeu', 'Oeu044549.2' => 'oeu', 'Oeu050063.1' => 'oeu', 'Oeu055801.1' => 'oeu', 'Oeu055802.1' => 'oeu', 'Os03g0804400' => 'osa', 'Os07g0200000' => 'osa', 'Os07g0568000' => 'osa', 'Os08g0566700' => 'osa', 'Peaxi162Scf00038g02453' => 'pax', 'Peaxi162Scf00129g00231' => 'pax', 'Peaxi162Scf00149g00918' => 'pax', 'Peaxi162Scf00415g00042' => 'pax', 'PGR031G3694' => 'pgr', 'PGR102G0119' => 'pgr', 'PGR102G0888' => 'pgr', 'PGR119G1793' => 'pgr', 'PGR119G2339' => 'pgr', 'PGSC0003DMG400002839' => 'stu', 'PGSC0003DMG400010361' => 'stu', 'PGSC0003DMG400024291' => 'stu', 'PGSC0003DMG401009187' => 'stu', 'Phvul.002G079800' => 'pvu', 'Phvul.002G099100' => 'pvu', 'Phvul.007G190500' => 'pvu', 'Phvul.008G256000' => 'pvu', 'Potri.008G009100' => 'ptr', 'Potri.010G249900' => 'ptr', 'Potri.012G120000' => 'ptr', 'Potri.014G195400' => 'ptr', 'Potri.015G118500' => 'ptr', 'Potri.015G119300' => 'ptr', 'Potri.016G063700' => 'ptr', 'Pp3c14_1460' => 'ppa', 'Pp3c15_1370' => 'ppa', 'Pp3c17_8270' => 'ppa', 'Pp3c1_20900' => 'ppa', 'Pp3c21_3770' => 'ppa', 'Pp3c24_8390' => 'ppa', 'Pp3c2_19180' => 'ppa', 'Pp3c9_2250' => 'ppa', 'PRCOL_00004119' => 'pco', 'Prupe.1G264200' => 'ppe', 'Prupe.3G167600' => 'ppe', 'Prupe.4G110000' => 'ppe', 'Prupe.8G218600' => 'ppe', 'Psat0s2227g0120' => 'psa', 'Psat6g061800' => 'psa', 'Psat7g130800' => 'psa', 'Psat7g263800' => 'psa', 'PSO017G2188' => 'pso', 'PSO063G1600' => 'pso', 'PSO170G4682' => 'pso', 'PSO210G4131' => 'pso', 'PSO541G2444' => 'pso', 'PSO675G8356' => 'pso', 'PSO782G0525' => 'pso', 'PSO832G1916' => 'pso', 'QL03p066646' => 'qlo', 'QL05p083372' => 'qlo', 'QL09p040867' => 'qlo', 'QL11p018085' => 'qlo', 'RcHm_v2.0_Chr2g0150201' => 'rch', 'RcHm_v2.0_Chr4g0445151' => 'rch', 'RcHm_v2.0_Chr5g0019861' => 'rch', 'RcHm_v2.0_Chr6g0287281' => 'rch', 'Rhsim08G0247800' => 'rsi', 'Rhsim12G0128100' => 'rsi', 'Rhsim13G0131700' => 'rsi', 'RhsimUnG0232100' => 'rsi', 'RhsimUnG0234400' => 'rsi', 'Sabra08G0005200' => 'sbr', 'Sabra10G0194400' => 'sbr', 'Sabra12G0088900' => 'sbr', 'Sabra14G0131300' => 'sbr', 'Sabra14G0144600' => 'sbr', 'Sabra15G0136700' => 'sbr', 'SalBow2G0888' => 'sbo', 'SalBow2G1614' => 'sbo', 'SalBow4G1888' => 'sbo', 'SalBow5G0549' => 'sbo', 'SalBow5G0662' => 'sbo', 'SalBow6G0074' => 'sbo', 'SalBow8G0281' => 'sbo', 'SalBow8G5470' => 'sbo', 'Sc04g0008620' => 'sci', 'Sc05g0005740' => 'sci', 'Sc15g0000910' => 'sci', 'Sed0004296' => 'sed', 'Sed0007440' => 'sed', 'Sed0015181' => 'sed', 'Sed0019240' => 'sed', 'Sed0028235' => 'sed', 'SEGI_00706' => 'sgi', 'SEGI_05255' => 'sgi', 'SEGI_10488' => 'sgi', 'SEGI_20495' => 'sgi', 'SEGI_30684' => 'sgi', 'SEGI_40754' => 'sgi', 'SEGI_41593' => 'sgi', 'SGA_v2.0_scaffold122G33291' => 'sas', 'SGA_v2.0_scaffold22G09966' => 'sas', 'SGA_v2.0_scaffold22G09972' => 'sas', 'SGA_v2.0_scaffold298G47679' => 'sas', 'SGA_v2.0_scaffold3G01730' => 'sas', 'SGA_v2.0_scaffold4818G54540' => 'sas', 'SGA_v2.0_scaffold71G24013' => 'sas', 'SGA_v2.0_scaffold754G53554' => 'sas', 'SGA_v2.0_scaffold754G53555' => 'sas', 'SGA_v2.0_scaffold754G53557' => 'sas', 'SHI20910' => 'shi', 'SHI21228' => 'shi', 'SMO116G0348' => 'smo', 'SMO137G0062' => 'smo', 'Solyc02g069080.4' => 'sly', 'Solyc03g123870.3' => 'sly', 'Solyc04g005850.1' => 'sly', 'Solyc09g072720.3' => 'sly', 'Sopen02g018180' => 'spe', 'Sopen03g041610' => 'spe', 'Sopen04g001900' => 'spe', 'Sopen09g028530' => 'spe', 'Sp1g08810' => 'spa', 'Sp1g08990' => 'spa', 'Sp6g11280' => 'spa', 'TAR365G0247' => 'tar', 'TAR365G1105' => 'tar', 'TAR369G1127' => 'tar', 'TAR383G0688' => 'tar', 'TAR383G0765' => 'tar', 'TAR624G1248' => 'tar', 'TAR626G0550' => 'tar', 'TAR626G1187' => 'tar', 'TAR626G1357' => 'tar', 'THA.LOC104800315' => 'tha', 'THA.LOC104806641' => 'tha', 'THA.LOC104812712' => 'tha', 'THA.LOC104816729' => 'tha', 'THA.LOC109116605' => 'tha', 'Thecc.01G253200' => 'tca', 'Thecc.02G236100' => 'tca', 'Thecc.06G015900' => 'tca', 'Thecc.06G016100' => 'tca', 'Thecc.06G140100' => 'tca', 'Thecc.06G140900' => 'tca', 'Thecc.06G141000' => 'tca', 'Thhalv10006875m.g' => 'esa', 'Thhalv10009913m.g' => 'esa', 'Thhalv10012711m.g' => 'esa', 'TPR.G10769' => 'tpr', 'TPR.G20981' => 'tpr', 'TPR.G38786' => 'tpr', 'TPR.G5664' => 'tpr', 'TWI12G0046' => 'twi', 'TWI12G1085' => 'twi', 'TWI18G0399' => 'twi', 'TWI36G0050' => 'twi', 'TWI63G0037' => 'twi', 'unitig_32.g11670' => 'ugi', 'unitig_32.g11671' => 'ugi', 'unitig_748.g7477' => 'ugi', 'unitig_748.g7478' => 'ugi', 'unitig_8.g2946' => 'ugi', 'vmacro03506' => 'vma', 'vmacro16311' => 'vma', 'vmacro18692' => 'vma', 'vmacro18762' => 'vma', 'vmacro18764' => 'vma', 'VMungo0251G1176' => 'vmu', 'VMungo0647G0339' => 'vmu', 'VMungo0720G1599' => 'vmu', 'VMungo1127G1399' => 'vmu', 'VMungo1215G2481' => 'vmu', 'Zm00001eb025360' => 'zma', 'Zm00001eb038690' => 'zma', 'Zm00001eb116310' => 'zma', 'Zm00001eb212640' => 'zma', 'Zm00001eb224310' => 'zma', 'Zm00001eb302800' => 'zma', 'Zm00001eb324620' => 'zma' ) $gf_id = 'HOM05D001270' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001270' ) $data_identifier = 'HOM05D001270' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 7, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 7, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 8, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 10, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324620' $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